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- PDB-1ern: NATIVE STRUCTURE OF THE EXTRACELLULAR DOMAIN OF ERYTHROPOIETIN (E... -

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Basic information

Entry
Database: PDB / ID: 1ern
TitleNATIVE STRUCTURE OF THE EXTRACELLULAR DOMAIN OF ERYTHROPOIETIN (EPO) RECEPTOR [EBP]
ComponentsPROTEIN (ERYTHROPOIETIN RECEPTOR)
KeywordsCYTOKINE / ERYTHROPOIETIN RECEPTOR / SIGNAL TRANSDUCTION / CYTOKINE RECEPTOR CLASS 1
Function / homology
Function and homology information


erythropoietin receptor activity / Signaling by Erythropoietin / Erythropoietin activates STAT5 / Erythropoietin activates Phospholipase C gamma (PLCG) / erythropoietin-mediated signaling pathway / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / decidualization / Erythropoietin activates RAS / brain development / cytokine-mediated signaling pathway ...erythropoietin receptor activity / Signaling by Erythropoietin / Erythropoietin activates STAT5 / Erythropoietin activates Phospholipase C gamma (PLCG) / erythropoietin-mediated signaling pathway / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / decidualization / Erythropoietin activates RAS / brain development / cytokine-mediated signaling pathway / heart development / nuclear speck / external side of plasma membrane / positive regulation of cell population proliferation / signal transduction / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Erythropoietin receptor / Long hematopoietin receptor, single chain, conserved site / Growth hormone/erythropoietin receptor, ligand binding / Erythropoietin receptor, ligand binding / Long hematopoietin receptor, single chain family signature. / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily ...Erythropoietin receptor / Long hematopoietin receptor, single chain, conserved site / Growth hormone/erythropoietin receptor, ligand binding / Erythropoietin receptor, ligand binding / Long hematopoietin receptor, single chain family signature. / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Erythropoietin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLivnah, O. / Stura, E.A. / Wilson, I.A.
Citation
Journal: Science / Year: 1999
Title: Crystallographic evidence for preformed dimers of erythropoietin receptor before ligand activation.
Authors: Livnah, O. / Stura, E.A. / Middleton, S.A. / Johnson, D.L. / Jolliffe, L.K. / Wilson, I.A.
#1: Journal: Science / Year: 1996
Title: Functional Mimicry of a Protein Hormone by a Peptide Agonist: The Epo Receptor Complex at 2.8 A
Authors: Livnah, O. / Stura, E.A. / Johnson, D.L. / Middleton, S.A. / Mulcahy, L.S. / Wrighton, N.C. / Dower, W.J. / Jolliffe, L.K. / Wilson, I.A.
History
DepositionJan 11, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 7, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ERYTHROPOIETIN RECEPTOR)
B: PROTEIN (ERYTHROPOIETIN RECEPTOR)


Theoretical massNumber of molelcules
Total (without water)47,0232
Polymers47,0232
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-10 kcal/mol
Surface area20980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.760, 55.680, 58.430
Angle α, β, γ (deg.)62.65, 88.31, 74.97
Int Tables number1
Space group name H-MP1

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Components

#1: Protein PROTEIN (ERYTHROPOIETIN RECEPTOR) / EBP


Mass: 23511.660 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P19235
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.2 %
Crystal growpH: 7.7 / Details: pH 7.7
Crystal grow
*PLUS
Temperature: 22.5 ℃ / pH: 7.8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.84-0.9 Mammonium sulfate1reservoir
20.1 Mimidazole1reservoir

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Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 14951 / % possible obs: 98 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rsym value: 0.059 / Net I/σ(I): 9.3
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.28 / % possible all: 97
Reflection
*PLUS
Rmerge(I) obs: 0.059
Reflection shell
*PLUS
% possible obs: 97 % / Rmerge(I) obs: 0.28

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.3refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EBP

1ebp


Resolution: 2.4→50 Å / Cross valid method: R-FREE / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.295 1423 5 %RANDOM
Rwork0.2158 ---
obs0.2158 13894 86 %-
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3240 0 0 97 3337
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARHCSDX.PRO
X-RAY DIFFRACTION2WATER.PARAM
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.216 / Rfactor Rwork: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

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